Construction of a high-density genetic linkage map and QTL mapping for bioenergy-related traits in sweet sorghum [Sorghum bicolor (L.) Moench]

Sorghum is an important but arguably undervalued cereal crop, grown in large areas in Asia and Africa due to its natural resilience to drought and heat. There is growing demand for sweet sorghum as a source of bioethanol as well as food and feed. The improvement of bioenergy-related traits directly affects bioethanol production from sweet sorghum; therefore, understanding the genetic basis of these traits would enable new cultivars to be developed for bioenergy production. In order to reveal the genetic architecture behind bioenergy-related traits, we generated an F2 population from a cross between sweet sorghum cv. ‘Erdurmus’ and grain sorghum cv. ‘Ogretmenoglu’. This was used to construct a genetic map from SNPs discovered by double-digest restriction-site associated DNA sequencing (ddRAD-seq). F3 lines derived from each F2 individual were phenotyped for bioenergy-related traits in two different locations and their genotypes were analyzed with the SNPs to identify QTL regions. On chromosomes 1, 7, and 9, three major plant height (PH) QTLs (qPH1.1, qPH7.1, and qPH9.1) were identified, with phenotypic variation explained (PVE) ranging from 10.8 to 34.8%. One major QTL (qPJ6.1) on chromosome 6 was associated with the plant juice trait (PJ) and explained 35.2% of its phenotypic variation. For fresh biomass weight (FBW), four major QTLs (qFBW1.1, qFBW6.1, qFBW7.1, and qFBW9.1) were determined on chromosomes 1, 6, 7, and 9, which explained 12.3, 14.5, 10.6, and 11.9% of the phenotypic variation, respectively. Moreover, two minor QTLs (qBX3.1 and qBX7.1) of Brix (BX) were mapped on chromosomes 3 and 7, explaining 8.6 and 9.7% of the phenotypic variation, respectively. The QTLs in two clusters (qPH7.1/qBX7.1 and qPH7.1/qFBW7.1) overlapped for PH, FBW and BX. The QTL, qFBW6.1, has not been previously reported. In addition, eight SNPs were converted into cleaved amplified polymorphic sequences (CAPS) markers, which can be easily detected by agarose gel electrophoresis. These QTLs and molecular markers can be used for pyramiding and marker-assisted selection studies in sorghum, to develop advanced lines that include desirable bioenergy-related traits

Inheritance of Indehiscent Capsule Character, Heritability and Genetic Advance Analyses in the Segregation Generations of Dehiscent x Indehiscent Capsules in Sesame

The investigation was made to estimate heritability and genetic advance and thus understand the genetic behavior of indehiscent capsule character in sesame with the field experiments during three consecutive years. Muganli-57 (♀) parent with dehiscent capsule was crossed with ACS 344 (♂), an introduction material, which had indehiscent capsule character. The results in the F1 generation indicated that dehiscent capsule character was dominant over indehiscent capsule. In F2, 3:1 segregation ratio was monitored and further confirmed in F3 showing indehiscent capsule character was controlled by a single recessive gene. Heritability was estimated by parent-offspring regression and the data were collected in F1, F2 and F3 generations derived from the cross between dehiscent and indehiscent capsule types. Heritability estimates in narrow sense for number of branches, number of capsules per plant, 1000 seed weight and seed yield were low in indehiscent capsule types of F2. Genetic advance had also low values except for number of branches (30.79%). Whilst low values obtained for indehiscent capsule, dehiscent capsule types in F2 indicated high heritability for the characters studied (70.52-92.84%). Stem height to the first capsule and plant height were of high heritabilities in both capsule types of F2 and F3. Although indehiscent capsule types had low means and heritabilities due to pleiotropic effects, mutant cross had heterotic effect on dehiscent types for all the characters. This positive shift could be explained by additive gene effect and this information presented in this investigation was therefore highly beneficial for the genetic improvement of sesame and reaching to high yielding types. This research also provides an example that bad parent may have a good progeny.

Genetic diversity and population structure of the Mediterranean sesame core collection with use of genome-wide SNPs developed by double digest RAD-Seq.

The Mediterranean sesame core collection contains agro-morphologically superior sesame accessions from geographically diverse regions in four continents. In the present investigation, the genetic diversity and population structure of this collection was analyzed with 5292 high-quality SNPs discovered by double-digest restriction site associated DNA (ddRAD) sequencing, a cost-effective and flexible next-generation sequencing method. The genetic distance between pairs of accessions varied from 0.023 to 0.524. The gene diversity was higher in accessions from Asia than from America, Africa, and Europe. The highest genetic differentiation was observed between accessions collected from America and Europe. Structure analysis showed the presence of three subpopulations among the sesame accessions, and only six accessions were placed in an admixture group. Phylogenetic tree and principal coordinate analysis clustered the accessions based on their countries of origin. However, no clear division was evident among the sesame accessions with regard to their continental locations. This result was supported by an AMOVA analysis, which revealed a genetic variation among continental groups of 5.53% of the total variation. The large number of SNPs clearly indicated that the Mediterranean sesame core collection is a highly diverse genetic resource. The collection can be exploited by breeders to select appropriate accessions that will provide high genetic gain in sesame improvement programs. The high-quality SNP data generated here should also be used in genome-wide association studies to explore qualitative trait loci and SNPs related to economically and agronomically important traits in sesame

A high-density SNP genetic map construction using ddRAD-Seq and mapping of capsule shattering trait in sesame

The seed-bearing capsule of sesame shatters at harvest. This wildish trait makes the crop unsuitable for mechanized harvesting and also restricts its commercial potential by limiting the cultivation for countries that have no access to low-cost labor. Therefore, the underlying genetic basis of the capsule shattering trait is highly important in order to develop mechanization-ready varieties for sustainable sesame farming. In the present study, we generated a sesame F2 population derived from a cross between a capsule shattering cultivar (Muganli-57) and a non-shattering mutant (PI 599446), which was used to construct a genetic map based on double-digest restriction-site-associated DNA sequencing. The resulting high-density genetic map contained 782 single-nucleotide polymorphisms (SNPs) and spanned a length of 697.3 cM, with an average marker interval of 0.89 cM. Based on the reference genome, the capsule shattering trait was mapped onto SNP marker S8_5062843 (78.9 cM) near the distal end of LG8 (chromosome 8). In order to reveal genes potentially controlling the shattering trait, the marker region (S8_5062843) was examined, and a candidate gene including six CDSs was identified. Annotation showed that the gene encodes a protein with 440 amino acids, sharing ∼99% homology with transcription repressor KAN1. Compared with the capsule shattering allele, the SNP change and altered splicing in the flanking region of S8_5062843 caused a frameshift mutation in the mRNA, resulting in the loss of function of this gene in the mutant parent and thus in non-shattering capsules and leaf curling. With the use of genomic data, InDel and CAPS markers were developed to differentiate shattering and non-shattering capsule genotypes in marker-assisted selection studies. The obtained results in the study can be beneficial in breeding programs to improve the shattering trait and enhance sesame productivity

Breeding history for shattering trait in sesame: classic to genomic approach

Sesame is an important oilseed crop that has high oil and protein content and unique antioxidant lignans. Capsule shattering at harvest is one of the most important problems affecting sesame production, with seed losses of up to 50%, making the crop unsuitable for mechanized harvesting. This paper provides an overview of breeding approaches addressing the capsule shattering trait in sesame and gives an outlook about the future perspectives of improvement for this trait. Sesame research has proceeded along the following parallel tracks: breeding for additional shatter resistance for manual harvest, breeding for mechanized harvest, and using molecular biology to improve the shatter resistance trait. In the future, genes controlling the shattering trait should be studied with techniques like RNA interference (RNAi), site-oriented mutagenesis, and gene editing with zinc finger nucleases (ZFNs) or CRISPR/Cas9, to develop new sesame varieties with capsules suitable for fully mechanized harvest

The advantages of intercropping to improve productivity in food and forage production – a review

Intercropping is an agricultural technique where many crops are grown together on the same field, and it is becoming more widely acknowledged for its ability to improve productivity in food and forage production. This farming method allows for the strategic integration of a profitable crop with cover or non-profitable crops to achieve reciprocal benefits, while also spreading advantages across different agricultural systems. Intercropping designs differ to attain greater crop yields, reduce the use of chemicals and fertilizers, and enhance water-use efficiency, especially in the demanding circumstances of arid and semi-arid countries. This study examines new mechanisms via which intercropping enhances sustainable agriculture, including recent progress in ecological, genetic, and microbial interactions that enhance plant growth and resilience. The adaptability of the Mediterranean region, for varied agricultural methods is also assessed, with a particular focus on the possibilities for implementing intercropping systems. This study provides a thorough analysis of existing research, emphasizing the many advantages of intercropping and its contribution to the progress of sustainable agriculture

Multiplex Real-Time qPCR Assay for Simultaneous and Sensitive Detection of Phytoplasmas in Sesame Plants and Insect Vectors

<div><p>Phyllody, a destructive and economically important disease worldwide caused by phytoplasma infections, is characterized by the abnormal development of floral structures into stunted leafy parts and contributes to serious losses in crop plants, including sesame (<i>Sesamum indicum</i> L.). Accurate identification, differentiation, and quantification of phyllody-causing phytoplasmas are essential for effective management of this plant disease and for selection of resistant sesame varieties. In this study, a diagnostic multiplex qPCR assay was developed using TaqMan^® chemistry based on detection of the 16S ribosomal RNA gene of phytoplasmas and the 18S ribosomal gene of sesame. Phytoplasma and sesame specific primers and probes labeled with different fluorescent dyes were used for simultaneous amplification of 16SrII and 16SrIX phytoplasmas in a single tube. The multiplex real-time qPCR assay allowed accurate detection, differentiation, and quantification of 16SrII and 16SrIX groups in 109 sesame plant and 92 insect vector samples tested. The assay was found to have a detection sensitivity of 1.8 x 10² and 1.6 x 10² DNA copies for absolute quantification of 16SrII and 16SrIX group phytoplasmas, respectively. Relative quantification was effective and reliable for determination of phyllody phytoplasma DNA amounts normalized to sesame DNA in infected plant tissues. The development of this qPCR assay provides a method for the rapid measurement of infection loads to identify resistance levels of sesame genotypes against phyllody phytoplasma disease.</p></div

Absolute and relative quantities of 16SrII and 16SrIX group phytoplasmas determined by qPCR in plant and insect samples tested in this study.

<p>Absolute and relative quantities of 16SrII and 16SrIX group phytoplasmas determined by qPCR in plant and insect samples tested in this study.</p

Multiplex qPCR detection of 16SrII and 16SrIX group phytoplasmas in plant and insect samples collected from different locations of Antalya province in Turkey.

<p>Multiplex qPCR detection of 16SrII and 16SrIX group phytoplasmas in plant and insect samples collected from different locations of Antalya province in Turkey.</p